php-4.4.2>make install
Installing PHP SAPI module: apache
Installing PHP CLI binary: /usr/local/php/bin/
Installing PHP CLI man page: /usr/local/php/man/man1/
Installing PEAR environment: /usr/local/php/lib/php/
[PEAR] Archive_Tar: bad md5sum for file /usr/local/php/lib/php/Archive/Tar.php
[PEAR] Console_Getopt: bad md5sum for file /usr/local/php/lib/php/Console/Getopt.php
[PEAR] HTML_Template_IT: bad md5sum for file /usr/local/php/lib/php/HTML/Template/IT.php
[PEAR] Net_UserAgent_Detect- already installed: 2.0.1
[PEAR] PEAR - already installed: 1.4.6
Wrote PEAR system config file at: /usr/local/php/etc/pear.conf
You may want to add: /usr/local/php/lib/php to your php.ini include_path
Installing build environment: /usr/local/php/lib/php/build/
Installing header files: /usr/local/php/include/php/
Installing helper programs: /usr/local/php/bin/
program: phpize
program: php-config
Installing man pages: /usr/local/php/man/man1/
page: phpize.1
page: php-config.1

So, where is the error? It just says that pear is already installed.
As for the "Archive_Tar: bad md5sum ", I think that you've already installed a beta release of php (from cvs?), so the stable release just complains.